8R3Y: Protein kinase C iota type

Cryo EM structure of a stable LGL/aPKC Iota/Par-6 complex. Determined by electron microscopy at 3.68 Å resolution. Released 20 Nov 2024.

Method: Electron microscopy
Resolution: 3.68 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,132
Mol. weight: 152.4 kDa
Ligands: ANP
Released: 20 Nov 2024

Explore 8R3Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R3Y contains 47 α-helices and 89 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain I: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	251-253	3
β-strand	255-262	8	1
β-strand	266-272	7	1
β-strand	279-286	8	1
α-helix	293-308	16
β-strand	318-322	5	1
β-strand	327-332	6	1
α-helix	333-335	3
β-strand	339	1	2
α-helix	340-347	8
α-helix	352-372	21
β-strand	375	1	3
β-strand	384-386	3	2
β-strand	392-394	3	2
β-strand	401	1	3
α-helix	404-405	2
β-strand	410	1	4
α-helix	422-426	5
β-strand	430	1	4
α-helix	433-448	16
α-helix	456	1
α-helix	459-460	2
β-strand	466	1	5
α-helix	467-476	10
β-strand	481-482	2	6
α-helix	487-497	11
α-helix	512-518	7
α-helix	520-523	4
α-helix	527-531	5
α-helix	536-537	2
α-helix	549-551	3
α-helix	554-557	4
α-helix	570-573	4

Chain L: 24 helices, 69 β-strands

Element	Residues	Length	Sheet
α-helix	18-21	4
β-strand	23-31	9	7
α-helix	34	1
β-strand	37-43	7	8
β-strand	48-53	6	8
β-strand	57-60	4	8
β-strand	68-71	4	8
β-strand	78-83	6	9
β-strand	89-94	6	9
β-strand	99-105	7	9
β-strand	110	1	10
β-strand	112-119	8	9
β-strand	141-144	4	11
β-strand	151-154	4	11
β-strand	160-163	4	11
β-strand	170-176	7	11
α-helix	178-183	6
β-strand	198-202	5	12
β-strand	210-215	6	12
β-strand	219-224	6	12
β-strand	229-234	6	12
α-helix	239	1
β-strand	240-243	4	13
β-strand	251-256	6	13
β-strand	261-265	5	13
β-strand	280	1	13
β-strand	291-296	6	14
β-strand	306-310	5	14
α-helix	314-317	4
β-strand	321-327	7	14
β-strand	330-336	7	14
β-strand	340-345	6	15
β-strand	360-365	6	15
β-strand	369-373	5	15
β-strand	381	1	15
α-helix	390-392	3
β-strand	395-401	7	16
α-helix	406-419	14
β-strand	436-437	2	10
α-helix	439-442	4
β-strand	447-452	6	16
β-strand	456-461	6	16
β-strand	469-474	6	16
α-helix	476-478	3
β-strand	479	1	17
α-helix	480-481	2
β-strand	500-503	4	14
β-strand	509-510	2	6
β-strand	517-523	7	18
α-helix	524-526	3
β-strand	528-533	6	18
β-strand	537-544	8	18
β-strand	548-550	3	19
α-helix	551-552	2
β-strand	553-557	5	18
α-helix	572-575	4
β-strand	576	1	17
α-helix	577-578	2
β-strand	581-583	3	19
β-strand	586-595	10	18
β-strand	603-607	5	20
β-strand	612-616	5	20
β-strand	620-625	6	20
β-strand	631-636	6	20
α-helix	656	1
β-strand	657	1	5
α-helix	658-659	2
β-strand	707-709	3	21
β-strand	723-731	9	22
β-strand	740-747	8	22
β-strand	751-758	8	22
β-strand	775-783	9	22
α-helix	788-789	2
β-strand	790-796	7	23
α-helix	801	1
β-strand	802	1	23
α-helix	803-805	3
α-helix	808-810	3
α-helix	816-818	3
α-helix	822-823	2
β-strand	824-829	6	23
β-strand	832-837	6	23
β-strand	840-848	9	23
α-helix	849-852	4
β-strand	857-866	10	24
β-strand	874-882	9	24
β-strand	887-891	5	24
β-strand	896-901	6	24
α-helix	909-912	4
β-strand	916-918	3	7
β-strand	922-928	7	7
β-strand	931-938	8	7
β-strand	947-948	2	10

Chain P: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	156-160	5	21
α-helix	167-169	3
β-strand	172-178	7	21
β-strand	189-194	6	21
α-helix	202-205	4
α-helix	213	1
β-strand	214-218	5	21
β-strand	221-222	2	21
α-helix	228-236	9
β-strand	242-246	5	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein kinase C iota type	I	protein	338	Homo sapiens	P41743 (AlphaFold model)
Lethal(2) giant larvae protein homolog 1	L	protein	937	Homo sapiens	Q15334 (AlphaFold model)
Partitioning defective 6 homolog alpha	P	protein	99	Homo sapiens	R4GMM2 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>8R3Y_1 Protein kinase C iota type (chains I)
SLGLQDFDLLRVIGRGSYAKVLLVRLKKTDRIYAMKVVKKELVNDDEDIDWVQTEKHVFE
QASNHPFLVGLHSCFQTESRLFFVIEYVNGGDLMFHMQRQRKLPEEHARFYSAEISLALN
YLHERGIIYRDLKLDNVLLDSEGHIKLTDYGMCKEGLRPGDTTSTFCGTPNYIAPEILRG
EDYGFSVDWWALGVLMFEMMAGRSPFDIVGSSDNPDQNTEDYLFQVILEKQIRIPRSLSV
KAASVLKSFLNKDPKERLGCHPQTGFADIQGHPFFRNVDWDMMEQKQVVPPFKPNISGEF
GLDNFDSQFTNEPVQLTPDDDDIVRKIDQSEFEGFEYI

Sequence of entity 2 (L), FASTA

>8R3Y_2 Lethal(2) giant larvae protein homolog 1 (chains L)
REKLKQELFAFNKTVEHGFPNQPSALAFDPELRIMAIGTRSGAVKIYGAPGVEFTGLHRD
AATVTQMHFLTGQGRLLSLLDDSSLHLWEIVHHNGCAHLEEALSFQLPSRPGFDGASAPL
SLTRVTVVLLVAAGDIAALGTEGSSVFFLDVTTLTLLEGQTLAPGEVLRSVPDDYRCGKA
LGPVESLQGHLRDPTKILIGYSRGLLVIWNQASQCVDHIFLGNQQLESLCWGRDSSTVVS
SHSDGSYAVWSVDAGSFPTLQPTVATTPYGPFPCKAINKILWRNCESGGHFIIFSGGMPR
ASYGDRHCVSVLRAETLVTLDFTSRIIDFFTVHSTRPEDEFDDPQALAVLLEEELVVLDL
QTPGWPAVPAPYLAPLHSSAITCSAHVASVPAKLWARIVSAGEQQSPQPVSSALSWPITG
GRNLAQEPSQRGLLLTGHEDGTVRFWDASGVALRPLYKLSTAGLFQTDCEHADSLAQAAE
DDWPPFRKVGCFDPYSDDPRLGVQKVALCKYTAQMVVAGTAGQVLVLELSDVPVEQAVSV
AIIDLLQDREGFTWKGHERLSPRTGPLPWPAGFQPRVLVQCLPPAAVTAVTLHTEWSLVA
FGTSHGFGLFDYQRKSPVLARCTLHPNDSLAMEGPLSRVKSLKKSLRQSFRRIRKSRVSG
KKRAANASSKLQEANAQLAEQACPHDVEMTPVQRRIEPRSADDSLSGVVRCLYFADTFLR
DGAHHGPTMWAGTNSGSVFAYALEVPAAAVGGEKRPEQAVEAVLGKEVQLMHRAPVVAIA
VLDGRGRPLPEPYEASRDLAQAPDMQGGHAVLIASEEQFKVFTLPKVSAKTKFKLTAHEG
CRVRKVALATFASVACEDYAETCLACLTNLGDVHVFSVPGLRPQVHYSCIRKEDISGIAS
CVFTRHGQGFYLISPSEFERFSLSARNITEPLCSLDI

Sequence of entity 3 (P), FASTA

>8R3Y_3 Partitioning defective 6 homolog alpha (chains P)
THRRVRLHKHGSDRPLGFYIRDGMSVRVAPQGLERVPGIFISRLVRGGLAESTGLLAVSD
EILEVNGIEVAGKTLDQVTDMMVANSHNLIVTVKPANQR

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1

Primary citation

Capture, mutual inhibition and release mechanism for aPKC-Par6 and its multisite polarity substrate Lgl. Earl, C.P., Cobbaut, M., Barros-Carvalho, A. et al. Nat Struct Mol Biol (2025) 32:729-739. DOI 10.1038/s41594-024-01425-0 · PubMed

Other PDB entries of the same protein (UniProt P41743 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1WMH 1.5 Å, Crystal structure of a PB1 domain complex of Protein kinase c iota and Par6 alpha
5LI9 1.79 Å, Structure of a nucleotide-bound form of PKCiota core kinase domain
3A8X 2.0 Å, Crystal Structure of PKCiota kinase domain
5LI1 2.0 Å, Structure of a Par3-inhibitory peptide bound to PKCiota core kinase domain
3A8W 2.1 Å, Crystal Structure of PKCiota kinase domain
8R3X 2.59 Å, Crystal structure of aPKC Iota kinase domain with LLGL2 peptide
3ZH8 2.74 Å, A novel small molecule aPKC inhibitor
1ZRZ 3.0 Å, Crystal Structure of the Catalytic Domain of Atypical Protein Kinase C-iota
9EJK 3.08 Å, Lgl2 bound to the aPKCiota-Par6b complex in nucleotide-free form. Head sub-complex…
5LIH 3.25 Å, Structure of a peptide-substrate bound to PKCiota core kinase domain
6ILZ 3.26 Å, Crystal structure of PKCiota in complex with inhibitor
9EJM 3.33 Å, Lgl2 bound to the aPKCiota-Par6B complex in its ADP-bound form

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